Fix NameError from TYPE_CHECKING annotations evaluated at runtime

[Mia1Gohary]

Several modules imported types (e.g. Molecule, Atom, ARCSpecies) only under if TYPE_CHECKING:, but referenced them unquoted in real function/class signatures. Since those names never exist at runtime, importing arc.common (and transitively the rest of the package) raised NameError. Same issue affected a few self-referencing class annotations (e.g. Level, SSHClient) and one genuinely missing import in parser.py.

Add from __future__ import annotations to defer annotation evaluation across all 53 affected files, and add the missing TYPE_CHECKING import for ARCSpecies in arc/parser/parser.py.

[alongd]

@Mia1Gohary, Thanks for digging into this!
My concern: the import-time NameError this fixes shouldn't happen on our Python 3.14 version, where annotation evaluation should be deferred by default. The crash is real on Python ≤ 3.13, but ARC doesn't support that anymore.

The fix here, I think, should be in arc/parser/parser.py: parse_active_space (line 536) annotates species: ARCSpecies, but ARCSpecies is imported nowhere in the module.
That's a static-analysis error worth fixing, with just a TYPE_CHECKING import, no future-import needed:

  from typing import TYPE_CHECKING
  if TYPE_CHECKING:
      from arc.species.species import ARCSpecies

Pleas reduce this PR to that one parser.py fix and drop from __future__ import annotations from the other 52 files